I had a foster male one time who had severe separation anxiety (his previous owners were retired during his whole life so they were always with him) and even having another dog around didn't help - they rarely played together. He was in his crate while I went to work - toys galore, special treats in a kong, calming sprays, etc. - and I did the "you must calm down before being let out of the crate" routine when I came home. My other dog was in a nearby crate so they could see and talk to each other. But he continued to try and chew his way out of the crate (I can't rebend the steel bars that he bent with his teeth and he was already 11 years old!). I tried to disappear for longer and longer periods of time to try and get him acclimated to being loose in the house but if I was gone more than 20 minutes he would start clawing at the doors trying to get out, he tore down the blinds on the patio doors, he toppled lamps trying to get out of the window. I spent money on a behaviorist - who told me to do exactly what I was doing (a waste of money she was) and after several months he started biting me if I tried to put him in the crate.
He was wonderful as long as I was around but the biting became too serious an issue. I cried when I took him back to the breeder (he ended up living out his days at her kennel) but I think that there are just some dogs and people combinations that simply don't work. If after several months things don't improve (and proper training has to be a component) one needs to reconsider the situation.
In this case KMac I think you are doing the right thing by seeking experienced help and things do sound better. In your case some of the problems are simply puppy behavior so maybe if you have the time and money an obedience class might be in order to help give him some structure. You might also try getting a bigger crate so he has more crate room or maybe an exercise pen so he can more around a bit more and chase his toys and release some energy.
